GENOME ANALYSIS REPORT

Data used in this analysis

In this experiment, the start set data are:

GENERAL DESCRIPTION

This report shows all the genome analysis information including:

The taxonomy identification of problematic strains as belonging to the Shewanella genus was based on Silva Taxonomy results (https://www.arb-silva.de/documentation/silva-taxonomy/). Species identification was performed using blastn of the 16S rRNA gene and by comparing the genomes of problematic strains against 129 complete genomes available in the NCBI database. The complete genome of Shewanella sp. Pdp11 and the partial genomes of pathogenic and saprophytic Shewanella strains were annotated using the DFAST tool. Functional annotation was performed based on Clusters of Orthologous Groups (COG), and the number of genes associated with each category was determined. Transposons were detected using the ISEScan tool (https://github.com/xiezhq/ISEScan), complemented by the tp_finder workflow for the identification of transposases and disrupted proteins. Genomic islands and Prophage were identified using IslandViewer 4 and Virsorter (https://github.com/jiarong/VirSorter2), respectively, and the GI enrichment was analyzed using DEgenes Hunter (https://github.com/seoanezonjic/ExpHunterSuite). Comparative genome analysis between Shewanellasp. Pdp11 and pathogenic strains allowed the identification of specific genes present in pathogenic strains but absent in the probiotic strain.

Shewanella species assignation

16S RNA

The Table indicated the 16S RNA analysis of problem genomes was carried out by blatn. The top 10 for each strain with high identity and coverage value.

strain identity coverage NCBI strain
Pdp11 99.580 100 Shewanella vaxholmensis strain SP1S1-4 16S ribosomal RNA, partial sequence
Pdp11 99.580 100 Shewanella arctica (ex Qoura et al. 2014) (nom. illeg.) strain : 40-3 16S ribosomal RNA, partial sequence
Pdp11 99.580 100 Shewanella scandinavica strain SP2S1-2 16S ribosomal RNA, partial sequence
Pdp11 99.055 100 Shewanella hafniensis strain NBRC 100975 16S ribosomal RNA, partial sequence
Pdp11 99.160 100 Shewanella hafniensis strain P010 16S ribosomal RNA, partial sequence
Pdp11 99.160 100 Shewanella seohaensis strain S7-3 16S ribosomal RNA, partial sequence
Pdp11 98.950 100 Shewanella putrefaciens strain Hammer 95 16S ribosomal RNA, partial sequence
Pdp11 98.845 100 Shewanella putrefaciens strain ATCC 8071 16S ribosomal RNA, partial sequence
Pdp11 98.847 100 Shewanella baltica strain 63 16S ribosomal RNA, partial sequence
SdM1 99.483 100 Shewanella seohaensis strain S7-3 16S ribosomal RNA, partial sequence
SdM1 99.353 100 Shewanella vaxholmensis strain SP1S1-4 16S ribosomal RNA, partial sequence
SdM1 99.353 100 Shewanella arctica (ex Qoura et al. 2014) (nom. illeg.) strain : 40-3 16S ribosomal RNA, partial sequence
SdM1 99.353 100 Shewanella scandinavica strain SP2S1-2 16S ribosomal RNA, partial sequence
SdM1 99.224 100 Shewanella putrefaciens strain Hammer 95 16S ribosomal RNA, partial sequence
SdM1 98.965 100 Shewanella putrefaciens strain ATCC 8071 16S ribosomal RNA, partial sequence
SdM1 98.706 100 Shewanella hafniensis strain NBRC 100975 16S ribosomal RNA, partial sequence
SdM1 98.836 100 Shewanella hafniensis strain P010 16S ribosomal RNA, partial sequence
SdM1 98.708 100 Shewanella xiamenensis strain S4 16S ribosomal RNA, partial sequence
SdM2 99.107 100 Shewanella putrefaciens strain NBRC 3908 16S ribosomal RNA, partial sequence
SdM2 99.106 100 Shewanella putrefaciens strain ATCC 8071 16S ribosomal RNA, partial sequence
SdM2 99.018 100 Shewanella putrefaciens strain Hammer 95 16S ribosomal RNA, partial sequence
SdM2 98.839 100 Shewanella profunda strain LT13a 16S ribosomal RNA, partial sequence
SH12 99.326 100 Shewanella xiamenensis strain S4 16S ribosomal RNA, partial sequence
SH12 99.038 100 Shewanella oneidensis strain MR-1 16S ribosomal RNA, partial sequence
SH12 98.845 100 Shewanella oneidensis strain MR-1 16S ribosomal RNA, partial sequence
SH12 98.847 100 Shewanella putrefaciens strain Hammer 95 16S ribosomal RNA, partial sequence
SH16 99.174 100 Shewanella putrefaciens strain Hammer 95 16S ribosomal RNA, partial sequence
SH16 99.174 100 Shewanella arctica (ex Qoura et al. 2014) (nom. illeg.) strain : 40-3 16S ribosomal RNA, partial sequence
SH16 99.174 100 Shewanella scandinavica strain SP2S1-2 16S ribosomal RNA, partial sequence
SH16 99.071 100 Shewanella putrefaciens strain ATCC 8071 16S ribosomal RNA, partial sequence
SH16 99.071 100 Shewanella vaxholmensis strain SP1S1-4 16S ribosomal RNA, partial sequence
SH16 98.762 100 Shewanella putrefaciens strain NBRC 3908 16S ribosomal RNA, partial sequence
SH16 98.763 100 Shewanella xiamenensis strain S4 16S ribosomal RNA, partial sequence
SH4 99.217 100 Shewanella xiamenensis strain S4 16S ribosomal RNA, partial sequence
SH4 98.957 100 Shewanella oneidensis strain MR-1 16S ribosomal RNA, partial sequence
SH4 98.783 100 Shewanella oneidensis strain MR-1 16S ribosomal RNA, partial sequence
SH6 99.285 100 Shewanella putrefaciens strain Hammer 95 16S ribosomal RNA, partial sequence
SH6 99.081 100 Shewanella putrefaciens strain ATCC 8071 16S ribosomal RNA, partial sequence
SH6 99.081 100 Shewanella vaxholmensis strain SP1S1-4 16S ribosomal RNA, partial sequence
SH6 99.081 100 Shewanella arctica (ex Qoura et al. 2014) (nom. illeg.) strain : 40-3 16S ribosomal RNA, partial sequence
SH6 99.081 100 Shewanella scandinavica strain SP2S1-2 16S ribosomal RNA, partial sequence
SH6 98.774 100 Shewanella putrefaciens strain NBRC 3908 16S ribosomal RNA, partial sequence
SH6 98.878 100 Shewanella xiamenensis strain S4 16S ribosomal RNA, partial sequence
SH9 99.106 100 Shewanella putrefaciens strain Hammer 95 16S ribosomal RNA, partial sequence
SH9 98.833 100 Shewanella putrefaciens strain ATCC 8071 16S ribosomal RNA, partial sequence

Complete genome comparison

Pyani

Heatmaps represent the calculation of Average Nucleotide Identity (ANI) using MUMmer (NUCmer) to align the input sequences. The results provide the specific nucleotide identity (first heatmap) and coverage (second heatmap), both ranging from 0 to 1, between our eight studied strains and 129 complete genomes of the Shewanella genus available in NCBI. The probiotic Shewanella Pdp11 showed high identity and coverage with Shewanella baltica, while SH4 and SH12 were closely related to Shewanella xiamenensis. In contrast, SH6, SH16, SH9, and SdM1 exhibited similarity to Shewanella oncorhynchi.

Sybelia results

The figures represent the synteny blocks of our studies strains and those with the highest identity.

Custom comparisons

Synteny blocks of Pdp11 custom comparisons with Shewanella putrefaciens ATCC 8071 (left) and Shewanella baltica OS678 (right), described as reference genomes

Best genome match comparisons

Synteny blocks among our studied strains and their best match by Pyani, including Pdp11 compared with uncultured Shewanella (left), SdM1 with Shewanella sp. WE21 (center), and SdM2 with Shewanella putrefaciens YZ-J (right)

Additionally, SH12 (left) and SH4 (right) matched with Shewanella xiamenensis 8M38

SH9 (left), SH6 (center) and SH16 (right) matched with Shewanella oncorhynchi B

Genome annotation

The DFAST tool (https://dfast.ddbj.nig.ac.jp/) was used for the COG annotation of 136 complete genomes. The heatmaps represent the number of genes associated with each COG functional category (left heatmap) and the standardized number of genes relative to the total number of coding sequences (CDS) in each genome, expressed as a percentage (gene %) (right heatmap).

Transposon

The transposable elements (TEs) analized was performed using a custom workflow with ISEScan (https://github.com/xiezhq/ISEScan) and Tp finder. The results include the number of TEs identified in each genome (left bar plot), the standardized number of TEs relative to the number of coding sequences (CDS) (right bar plot), and the repeated TEs within each genome (Table). Additionally, the presence or absence of disrupted proteins (left heatmap) and transposases (right heatmap) in each genome was determined and represented by a binary matrix (0 and 1). The analysis identified the presence of TEs in 101 strains (more than 70% of the strains of this genus).

genome coordinate start tpfinder end tpfinder transposase protein disrupt protein
Shewanella Pdp11:850951:856278 2033 3326 A0A883CDA5 A0A4Y5YC98
Shewanella Pdp11:1261471:1266798 1992 3309 A0A883CDA5 A9KZG6
Shewanella Pdp11:1906106:1911827 2000 3723 A0AAE4PW88 A0AAJ2MQ60
Shewanella Pdp11:2693976:2700579 1969 4609 A0AAE4PZ99 A0A2G1ZI34
Shewanella Pdp11:2990403:2995648 1999 3241 Q8EF58 A3D7T2
Shewanella Pdp11:3053373:3058616 2049 3244 A0A9E6JBE3 A0AAW6QV90
Shewanella Pdp11:3073685:3079406 1999 3725 A0AAE4PW88 A0AAJ2J2I4
Shewanella Pdp11:4315854:4321181 2006 3320 A0A883CDA5 A0AAE4TJG1
Shewanella Pdp11:4349020:4355949 1959 3354 A0AAP2ZPU8 A0A6G9QQZ7

Genomic Island

The mobilome analysis included the identification of genomic islands (GIs) using IslandViewer4 (https://www.pathogenomics.sfu.ca/islandviewer/). The results show the total number of GIs identified in 134 research strains of Shewanella sp. The figure illustrates the number of genomic islands in which certain functional categories, determined by DFAST, are significant. Additionally, functional enrichment of GIs was performed using the ExpHunterSuite script clusters_to_enrichment.R, which is based on the clusterProfiler package, with an FDR threshold of 0.05 (-p 0.05). The heatmap represents the number of GIs assigned to COG categories (left) and this number standardized to the total GIs (GI %) (right).

Prophage

Prophage was analized using Virsorter (https://github.com/jiarong/VirSorter2). Prophages were identified in 77 complete genomes of Shewanella

Probiotic and pathogenic strains comparison

This analysis were focused on pathogenic and probiotic strains comparison by Tarsynflow, which identified the specific genes on pathogenic and their absent on probiotic strain.

Entry protein names organism
A0A073KRP2 L-lactate permease Shewanella xiamenensis
A0A380B106 L-seryl-tRNA(Sec) selenium transferase (EC 2.9.1.1) (Selenocysteine synthase) (Sec synthase) (Selenocysteinyl-tRNA(Sec) synthase) Shewanella morhuae
A0A1E3UTG5 DUF4274 domain-containing protein Shewanella xiamenensis
A0A1E3UVI4 LuxR C-terminal-related transcriptional regulator (LuxR family transcriptional regulator) Shewanella xiamenensis
A0A220US46 Two-component system response regulator Shewanella bicestrii
A0A2M7HTT6 Sodium:alanine symporter Shewanella sp. CG12_big_fil_rev_8_21_14_0_65_47_15
A0A4R2FB63 Succinate dehydrogenase/fumarate reductase flavoprotein subunit Shewanella fodinae
A0A4R2FJ85 Two-component system response regulator AdeR Shewanella fodinae
A0A501XHX2 CDP-glycerol--glycerophosphate glycerophosphotransferase Shewanella sp. LC6
A0A501XY11 Cytochrome c3 family protein Shewanella sp. LC6
A0A5B8QSE5 TetR/AcrR family transcriptional regulator Shewanella decolorationis
A0A6N3J9Z1 histidine kinase (EC 2.7.13.3) Shewanella sp. (strain W3-18-1)
A0A9X2WTL9 histidine kinase (EC 2.7.13.3) Shewanella septentrionalis
A0AAJ2J6D6 Atu1372/SO_1960 family protein Shewanella sp. SP1S1-7
A3D7Z8 Sodium/calcium exchanger membrane region Shewanella baltica (strain OS155 / ATCC BAA-1091)
A9KV88 Selenocysteine-specific translation elongation factor Shewanella baltica (strain OS195)